# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Apr  7 23:18:44 2020
#   Inital geometry file: a 155 line input string
#   Ligand name: 4-[2-(4-chlorophenyl)ethylamino]-~{N}-[4-(4-methylpiperazin-1-yl)phenyl]-2-oxidanylidene-1~{H}-pyridine-3-carboxamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CN1CCN(CC1)c2ccc(NC(=O)C3=C(NCCc4ccc(Cl)cc4)C=CNC3=O)cc2
#
data_comp_list
loop_
_chem_comp.id
_chem_comp.three_letter_code
_chem_comp.name
_chem_comp.group
_chem_comp.number_atoms_all
_chem_comp.number_atoms_nh
_chem_comp.desc_level
_chem_comp.initial_date
_chem_comp.modified_date
_chem_comp.source
 5Q2  5Q2  4-[2-(4-chlorophenyl)ethylamino]-~{N}-[4-(4-methylpiperazin-1-yl)phenyl]-2-oxidanylidene-1~{H}-pyridine-3-carboxamide  ligand  61  33  .  2021-08-04  2022-09-22
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_5Q2
loop_
_chem_comp_atom.comp_id
_chem_comp_atom.atom_id
_chem_comp_atom.type_symbol
_chem_comp_atom.type_energy
_chem_comp_atom.charge
_chem_comp_atom.partial_charge
_chem_comp_atom.x
_chem_comp_atom.y
_chem_comp_atom.z
 5Q2  C4   C   CH2   0  -0.308   -7.4957   0.6632   0.5354
 5Q2  C6   C   CH2   0  -0.313   -6.2515   2.6756   0.1278
 5Q2  C11  C   CR6   0   0.347   -2.6906  -0.9610   0.1475
 5Q2  C7   C   CH2   0  -0.278   -7.5214   3.3279  -0.3867
 5Q2  C8   C   CR6   0   0.349   -5.1138   0.5218   0.0428
 5Q2  C9   C   CR16  0  -0.316   -5.0756  -0.8433  -0.2767
 5Q2  C10  C   CR16  0  -0.343   -3.8984  -1.5608  -0.2229
 5Q2  C12  C   CR16  0  -0.302   -2.7181   0.3906   0.4797
 5Q2  C13  C   CR16  0  -0.350   -3.9077   1.1084   0.4319
 5Q2  N2   N   NT    0  -0.412   -8.6937   2.7671   0.2494
 5Q2  C3   C   CH2   0  -0.282   -8.7463   1.3402   0.0114
 5Q2  C1   C   CH3   0  -0.519   -9.9038   3.4284  -0.1809
 5Q2  N5   N   NT    0  -0.515   -6.3055   1.2420  -0.0713
 5Q2  C15  C   C     0   0.601   -0.2592  -1.4195   0.1387
 5Q2  O16  O   O     0  -0.530    0.0830  -0.2305   0.1178
 5Q2  C17  C   CR6   0  -0.456    0.7319  -2.5154   0.1157
 5Q2  C18  C   CR6   0   0.531    2.1218  -2.2123   0.0769
 5Q2  C19  C   CR16  0  -0.473    3.0637  -3.2874   0.0571
 5Q2  C20  C   CR16  0   0.063    2.6178  -4.5601   0.0744
 5Q2  N21  N   NR16  0  -0.668    1.3030  -4.8407   0.1054
 5Q2  C23  C   CR6   0   0.571    0.3083  -3.8878   0.1250
 5Q2  O24  O   O     0  -0.538   -0.8650  -4.2941   0.1483
 5Q2  N25  N   NH1   0  -0.693    2.5796  -0.9637   0.0574
 5Q2  C26  C   CH2   0  -0.255    3.9745  -0.5858   0.0137
 5Q2  C27  C   CH2   0  -0.560    4.0937   0.9344  -0.0387
 5Q2  C28  C   CR6   0   0.134    5.5330   1.3559  -0.1144
 5Q2  C29  C   CR16  0  -0.309    6.1845   1.4449  -1.3418
 5Q2  C30  C   CR16  0  -0.195    7.5224   1.8019  -1.4215
 5Q2  C31  C   CR6   0  -0.056    8.2179   2.0713  -0.2531
 5Q2  C32  C   CR16  0  -0.196    7.5976   1.9892   0.9832
 5Q2  C33  C   CR16  0  -0.311    6.2585   1.6303   1.0411
 5Q2  CL   CL  CL    0  -0.133    9.8911   2.5223  -0.3409
 5Q2  H1   H   HCH2  0   0.214   -7.4604   0.7610   1.6308
 5Q2  H2   H   HCH2  0   0.253   -7.5590  -0.3989   0.3081
 5Q2  H3   H   HCH2  0   0.250   -5.4107   3.0912  -0.4294
 5Q2  H4   H   HCH2  0   0.210   -6.1057   2.9374   1.1875
 5Q2  H5   H   HCH2  0   0.240   -7.4745   4.3990  -0.1762
 5Q2  H6   H   HCH2  0   0.192   -7.5602   3.2158  -1.4846
 5Q2  H7   H   HCR6  0   0.261   -5.9723  -1.3568  -0.5980
 5Q2  H8   H   HCR6  0   0.260   -3.9154  -2.6106  -0.4921
 5Q2  H9   H   HCR6  0   0.268   -1.8225   0.9011   0.7939
 5Q2  H10  H   HCR6  0   0.266   -3.8687   2.1490   0.7225
 5Q2  H12  H   HCH2  0   0.192   -8.8619   1.1095  -1.0623
 5Q2  H13  H   HCH2  0   0.239   -9.6140   0.9206   0.5263
 5Q2  H14  H   HCH3  0   0.192  -10.0895   3.3322  -1.2622
 5Q2  H15  H   HCH3  0   0.233  -10.7647   3.0111   0.3436
 5Q2  H16  H   HCH3  0   0.234   -9.8506   4.4928   0.0528
 5Q2  H17  H   HNH1  0   0.430   -1.7099  -2.7934   0.1537
 5Q2  H19  H   HCR6  0   0.295    4.1262  -3.1062   0.0336
 5Q2  H20  H   HCR6  0   0.320    3.2859  -5.4083   0.0612
 5Q2  H21  H   HNH1  0   0.424    1.8638  -0.2435   0.0746
 5Q2  H22  H   HCH2  0   0.249    4.5058  -0.9635   0.8932
 5Q2  H23  H   HCH2  0   0.248    4.4613  -1.0180  -0.8662
 5Q2  H24  H   HCH2  0   0.265    3.5491   1.3075  -0.9096
 5Q2  H25  H   HCH2  0   0.265    3.6238   1.3671   0.8479
 5Q2  H26  H   HCR6  0   0.261    5.6420   1.2386  -2.2568
 5Q2  H27  H   HCR6  0   0.279    8.0123   1.8736  -2.3831
 5Q2  H28  H   HCR6  0   0.279    8.1450   2.2045   1.8908
 5Q2  H29  H   HCR6  0   0.261    5.7731   1.5670   2.0076
 5Q2  H11  H   HNR6  0   0.424    1.0046  -5.8059   0.1211
 5Q2  N14  N   NH1   0  -0.787   -1.5595  -1.7826   0.1820

loop_
_chem_comp_bond.comp_id
_chem_comp_bond.atom_id_1
_chem_comp_bond.atom_id_2
_chem_comp_bond.type
_chem_comp_bond.value_dist
_chem_comp_bond.value_dist_esd
_chem_comp_bond.value_dist_neutron
 5Q2  CL   C31  single    1.735  0.020  1.735
 5Q2  C32  C33  aromatic  1.388  0.020  1.388
 5Q2  C32  C31  aromatic  1.386  0.020  1.386
 5Q2  C33  C28  aromatic  1.392  0.020  1.392
 5Q2  C31  C30  aromatic  1.386  0.020  1.386
 5Q2  C28  C29  aromatic  1.392  0.020  1.392
 5Q2  C28  C27  single    1.502  0.020  1.502
 5Q2  C30  C29  aromatic  1.387  0.020  1.387
 5Q2  C27  C26  single    1.526  0.020  1.526
 5Q2  C26  N25  single    1.446  0.020  1.446
 5Q2  C19  C20  double    1.349  0.020  1.349
 5Q2  C19  C18  single    1.430  0.020  1.430
 5Q2  C20  N21  single    1.345  0.020  1.345
 5Q2  N25  C18  single    1.330  0.020  1.330
 5Q2  C18  C17  double    1.423  0.020  1.423
 5Q2  N21  C23  single    1.378  0.020  1.378
 5Q2  C23  C17  single    1.436  0.020  1.436
 5Q2  C23  O24  double    1.242  0.020  1.242
 5Q2  C17  C15  single    1.478  0.020  1.478
 5Q2  C15  O16  double    1.237  0.020  1.237
 5Q2  C15  N14  single    1.351  0.020  1.351
 5Q2  N14  C11  single    1.398  0.020  1.398
 5Q2  C11  C10  aromatic  1.398  0.020  1.398
 5Q2  C11  C12  aromatic  1.392  0.020  1.392
 5Q2  C10  C9   aromatic  1.380  0.020  1.380
 5Q2  C12  C13  aromatic  1.390  0.020  1.390
 5Q2  C9   C8   aromatic  1.403  0.020  1.403
 5Q2  C13  C8   aromatic  1.396  0.020  1.396
 5Q2  C8   N5   single    1.397  0.020  1.397
 5Q2  N5   C6   single    1.448  0.020  1.448
 5Q2  N5   C4   single    1.456  0.020  1.456
 5Q2  C6   C7   single    1.518  0.020  1.518
 5Q2  C4   C3   single    1.516  0.020  1.516
 5Q2  C7   N2   single    1.447  0.020  1.447
 5Q2  C3   N2   single    1.448  0.020  1.448
 5Q2  N2   C1   single    1.445  0.020  1.445
 5Q2  C4   H1   single    0.970  0.020  1.090
 5Q2  C4   H2   single    0.970  0.020  1.090
 5Q2  C6   H3   single    0.970  0.020  1.090
 5Q2  C6   H4   single    0.970  0.020  1.090
 5Q2  C7   H5   single    0.970  0.020  1.090
 5Q2  C7   H6   single    0.970  0.020  1.090
 5Q2  C9   H7   single    0.930  0.020  1.080
 5Q2  C10  H8   single    0.930  0.020  1.080
 5Q2  C12  H9   single    0.930  0.020  1.080
 5Q2  C13  H10  single    0.930  0.020  1.080
 5Q2  C3   H12  single    0.970  0.020  1.090
 5Q2  C3   H13  single    0.970  0.020  1.090
 5Q2  C1   H14  single    0.970  0.020  1.090
 5Q2  C1   H15  single    0.970  0.020  1.090
 5Q2  C1   H16  single    0.970  0.020  1.090
 5Q2  N14  H17  single    0.860  0.020  1.020
 5Q2  C19  H19  single    0.930  0.020  1.080
 5Q2  C20  H20  single    0.930  0.020  1.080
 5Q2  N25  H21  single    0.860  0.020  1.020
 5Q2  C26  H22  single    0.970  0.020  1.090
 5Q2  C26  H23  single    0.970  0.020  1.090
 5Q2  C27  H24  single    0.970  0.020  1.090
 5Q2  C27  H25  single    0.970  0.020  1.090
 5Q2  C29  H26  single    0.930  0.020  1.080
 5Q2  C30  H27  single    0.930  0.020  1.080
 5Q2  C32  H28  single    0.930  0.020  1.080
 5Q2  C33  H29  single    0.930  0.020  1.080
 5Q2  N21  H11  single    0.860  0.020  1.020

loop_
_chem_comp_angle.comp_id
_chem_comp_angle.atom_id_1
_chem_comp_angle.atom_id_2
_chem_comp_angle.atom_id_3
_chem_comp_angle.value_angle
_chem_comp_angle.value_angle_esd
 5Q2  H2   C4   H1   107.25  3.000
 5Q2  H2   C4   N5   110.41  3.000
 5Q2  H1   C4   N5   110.69  3.000
 5Q2  H2   C4   C3   108.41  3.000
 5Q2  H1   C4   C3   109.32  3.000
 5Q2  N5   C4   C3   110.67  3.000
 5Q2  H4   C6   H3   107.39  3.000
 5Q2  H4   C6   N5   111.88  3.000
 5Q2  H3   C6   N5   109.61  3.000
 5Q2  H4   C6   C7   109.56  3.000
 5Q2  H3   C6   C7   107.94  3.000
 5Q2  N5   C6   C7   110.34  3.000
 5Q2  N14  C11  C12  125.49  3.000
 5Q2  C12  C11  C10  117.55  3.000
 5Q2  N14  C11  C10  116.94  3.000
 5Q2  H6   C7   H5   107.02  3.000
 5Q2  H6   C7   N2   111.67  3.000
 5Q2  H5   C7   N2   109.28  3.000
 5Q2  H6   C7   C6   108.83  3.000
 5Q2  H5   C7   C6   108.67  3.000
 5Q2  N2   C7   C6   111.24  3.000
 5Q2  N5   C8   C13  122.88  3.000
 5Q2  N5   C8   C9   120.42  3.000
 5Q2  C13  C8   C9   116.67  3.000
 5Q2  H7   C9   C10  118.16  3.000
 5Q2  H7   C9   C8   120.46  3.000
 5Q2  C10  C9   C8   121.36  3.000
 5Q2  H8   C10  C9   118.73  3.000
 5Q2  H8   C10  C11  119.65  3.000
 5Q2  C9   C10  C11  121.62  3.000
 5Q2  H9   C12  C13  118.46  3.000
 5Q2  H9   C12  C11  120.87  3.000
 5Q2  C13  C12  C11  120.66  3.000
 5Q2  H10  C13  C12  117.19  3.000
 5Q2  H10  C13  C8   120.69  3.000
 5Q2  C12  C13  C8   122.12  3.000
 5Q2  C1   N2   C3   111.83  3.000
 5Q2  C1   N2   C7   111.73  3.000
 5Q2  C3   N2   C7   109.83  3.000
 5Q2  H13  C3   H12  107.15  3.000
 5Q2  H13  C3   N2   109.26  3.000
 5Q2  H12  C3   N2   111.69  3.000
 5Q2  H13  C3   C4   108.71  3.000
 5Q2  H12  C3   C4   109.22  3.000
 5Q2  N2   C3   C4   110.70  3.000
 5Q2  H16  C1   H15  107.98  3.000
 5Q2  H16  C1   H14  107.68  3.000
 5Q2  H15  C1   H14  107.79  3.000
 5Q2  H16  C1   N2   110.00  3.000
 5Q2  H15  C1   N2   110.04  3.000
 5Q2  H14  C1   N2   113.19  3.000
 5Q2  C8   N5   C6   117.85  3.000
 5Q2  C6   N5   C4   111.52  3.000
 5Q2  C8   N5   C4   117.28  3.000
 5Q2  C17  C15  O16  121.79  3.000
 5Q2  O16  C15  N14  121.67  3.000
 5Q2  C17  C15  N14  116.54  3.000
 5Q2  C23  C17  C18  119.45  3.000
 5Q2  C23  C17  C15  120.71  3.000
 5Q2  C18  C17  C15  119.84  3.000
 5Q2  N25  C18  C19  118.62  3.000
 5Q2  N25  C18  C17  122.45  3.000
 5Q2  C19  C18  C17  118.93  3.000
 5Q2  H19  C19  C20  119.00  3.000
 5Q2  H19  C19  C18  121.55  3.000
 5Q2  C20  C19  C18  119.45  3.000
 5Q2  H20  C20  N21  116.19  3.000
 5Q2  H20  C20  C19  122.45  3.000
 5Q2  N21  C20  C19  121.37  3.000
 5Q2  H11  N21  C23  116.56  3.000
 5Q2  H11  N21  C20  119.24  3.000
 5Q2  C23  N21  C20  124.19  3.000
 5Q2  O24  C23  N21  117.14  3.000
 5Q2  O24  C23  C17  126.26  3.000
 5Q2  N21  C23  C17  116.61  3.000
 5Q2  H21  N25  C26  119.68  3.000
 5Q2  H21  N25  C18  115.02  3.000
 5Q2  C26  N25  C18  125.30  3.000
 5Q2  H23  C26  H22  107.08  3.000
 5Q2  H23  C26  C27  109.33  3.000
 5Q2  H22  C26  C27  109.48  3.000
 5Q2  H23  C26  N25  110.50  3.000
 5Q2  H22  C26  N25  110.72  3.000
 5Q2  C27  C26  N25  109.68  3.000
 5Q2  H25  C27  H24  107.28  3.000
 5Q2  H25  C27  C28  110.00  3.000
 5Q2  H24  C27  C28  109.97  3.000
 5Q2  H25  C27  C26  109.45  3.000
 5Q2  H24  C27  C26  109.18  3.000
 5Q2  C28  C27  C26  110.87  3.000
 5Q2  C33  C28  C29  118.38  3.000
 5Q2  C29  C28  C27  120.72  3.000
 5Q2  C33  C28  C27  120.87  3.000
 5Q2  H26  C29  C30  118.91  3.000
 5Q2  H26  C29  C28  119.87  3.000
 5Q2  C30  C29  C28  121.23  3.000
 5Q2  H27  C30  C31  120.61  3.000
 5Q2  H27  C30  C29  120.34  3.000
 5Q2  C31  C30  C29  119.05  3.000
 5Q2  CL   C31  C32  119.49  3.000
 5Q2  C32  C31  C30  121.06  3.000
 5Q2  CL   C31  C30  119.45  3.000
 5Q2  H28  C32  C33  120.32  3.000
 5Q2  H28  C32  C31  120.69  3.000
 5Q2  C33  C32  C31  118.99  3.000
 5Q2  H29  C33  C32  118.99  3.000
 5Q2  H29  C33  C28  119.71  3.000
 5Q2  C32  C33  C28  121.29  3.000
 5Q2  H17  N14  C15  113.98  3.000
 5Q2  H17  N14  C11  117.47  3.000
 5Q2  C15  N14  C11  128.31  3.000

loop_
_chem_comp_tor.comp_id
_chem_comp_tor.id
_chem_comp_tor.atom_id_1
_chem_comp_tor.atom_id_2
_chem_comp_tor.atom_id_3
_chem_comp_tor.atom_id_4
_chem_comp_tor.value_angle
_chem_comp_tor.value_angle_esd
_chem_comp_tor.period
 5Q2  CONST_01  C8   C9   C10  C11     0.00   0.0  0
 5Q2  CONST_02  C8   C13  C12  C11     0.00   0.0  0
 5Q2  CONST_03  C12  C11  C10  C9      0.00   0.0  0
 5Q2  CONST_04  C12  C13  C8   C9      0.00   0.0  0
 5Q2  CONST_05  C13  C12  C11  C10     0.00   0.0  0
 5Q2  CONST_06  C13  C8   C9   C10     0.00   0.0  0
 5Q2  CONST_07  C31  C32  C33  C28     0.00   0.0  0
 5Q2  CONST_08  C31  C30  C29  C28     0.00   0.0  0
 5Q2  CONST_09  C32  C33  C28  C29     0.00   0.0  0
 5Q2  CONST_10  C32  C31  C30  C29     0.00   0.0  0
 5Q2  CONST_11  C33  C32  C31  C30     0.00   0.0  0
 5Q2  CONST_12  C33  C28  C29  C30     0.00   0.0  0
 5Q2  CONST_13  N5   C8   C9   C10   180.00   0.0  0
 5Q2  CONST_14  N5   C8   C13  C12   180.00   0.0  0
 5Q2  CONST_15  C20  N21  C23  C17     0.00   0.0  0
 5Q2  CONST_16  N14  C11  C10  C9    180.00   0.0  0
 5Q2  CONST_17  N14  C11  C12  C13   180.00   0.0  0
 5Q2  CONST_18  C32  C33  C28  C27   180.00   0.0  0
 5Q2  CONST_19  C30  C29  C28  C27   180.00   0.0  0
 5Q2  CONST_20  CL   C31  C30  C29   180.00   0.0  0
 5Q2  CONST_21  CL   C31  C32  C33   180.00   0.0  0
 5Q2  CONST_22  O24  C23  N21  C20   180.00   0.0  0
 5Q2  CONST_23  H7   C9   C10  C11   180.00   0.0  0
 5Q2  CONST_24  H10  C13  C12  C11   180.00   0.0  0
 5Q2  CONST_25  H8   C10  C9   C8    180.00   0.0  0
 5Q2  CONST_26  H9   C12  C13  C8    180.00   0.0  0
 5Q2  CONST_27  H28  C32  C33  C28   180.00   0.0  0
 5Q2  CONST_28  H27  C30  C29  C28   180.00   0.0  0
 5Q2  CONST_29  H29  C33  C28  C29   180.00   0.0  0
 5Q2  CONST_30  H26  C29  C30  C31   180.00   0.0  0
 5Q2  CONST_31  H11  N21  C23  C17   180.00   0.0  0
 5Q2  CONST_32  C17  C15  N14  C11   180.00   0.0  0
 5Q2  CONST_35  H17  N14  C11  C10     0.00   0.0  0
 5Q2  CONST_36  O16  C15  N14  C11     0.00   0.0  0
 5Q2  Var_01    C9   C8   N5   C4     49.09  30.0  1
 5Q2  Var_02    C7   C6   N5   C4    -55.07  30.0  1
 5Q2  Var_03    C7   N2   C3   C4     58.23  30.0  1
 5Q2  Var_04    C3   C4   N5   C6     55.48  30.0  1
 5Q2  Var_05    C3   N2   C7   C6    -58.32  30.0  1
 5Q2  Var_06    N5   C6   C7   N2     56.73  30.0  1
 5Q2  Var_07    N5   C4   C3   N2    -56.91  30.0  1
 5Q2  Var_08    C18  C17  C15  N14  -179.68  30.0  2
 5Q2  Var_09    C26  N25  C18  C17  -179.79  30.0  1
 5Q2  Var_10    C33  C28  C27  C26   -91.85  30.0  2
 5Q2  Var_11    H14  C1   N2   C7     61.54  30.0  3
 5Q2  Var_12    C27  C26  N25  C18   178.33  30.0  2
 5Q2  Var_13    C28  C27  C26  N25  -178.79  30.0  1

loop_
_chem_comp_plane_atom.comp_id
_chem_comp_plane_atom.plane_id
_chem_comp_plane_atom.atom_id
_chem_comp_plane_atom.dist_esd
 5Q2  plan-1  C11  0.020
 5Q2  plan-1  C8   0.020
 5Q2  plan-1  C9   0.020
 5Q2  plan-1  C10  0.020
 5Q2  plan-1  C12  0.020
 5Q2  plan-1  C13  0.020
 5Q2  plan-1  N5   0.020
 5Q2  plan-1  H7   0.020
 5Q2  plan-1  H8   0.020
 5Q2  plan-1  H9   0.020
 5Q2  plan-1  H10  0.020
 5Q2  plan-1  N14  0.020
 5Q2  plan-2  C15  0.020
 5Q2  plan-2  C17  0.020
 5Q2  plan-2  C18  0.020
 5Q2  plan-2  C19  0.020
 5Q2  plan-2  C20  0.020
 5Q2  plan-2  N21  0.020
 5Q2  plan-2  C23  0.020
 5Q2  plan-2  O24  0.020
 5Q2  plan-2  N25  0.020
 5Q2  plan-2  H19  0.020
 5Q2  plan-2  H20  0.020
 5Q2  plan-2  H11  0.020
 5Q2  plan-3  C27  0.020
 5Q2  plan-3  C28  0.020
 5Q2  plan-3  C29  0.020
 5Q2  plan-3  C30  0.020
 5Q2  plan-3  C31  0.020
 5Q2  plan-3  C32  0.020
 5Q2  plan-3  C33  0.020
 5Q2  plan-3  CL   0.020
 5Q2  plan-3  H26  0.020
 5Q2  plan-3  H27  0.020
 5Q2  plan-3  H28  0.020
 5Q2  plan-3  H29  0.020
 5Q2  plan-4  C11  0.020
 5Q2  plan-4  C15  0.020
 5Q2  plan-4  O16  0.020
 5Q2  plan-4  C17  0.020
 5Q2  plan-4  H17  0.020
 5Q2  plan-4  N14  0.020

